Cyclin Based Inhibitors of CDK2 and CDK4

ABSTRACT

Structural and functional analysis of peptide inhibitor binding to the cyclin D1 groove has been investigated and used to design peptides that provide the basis for structure-activity relationships, have improved binding and have potential for development as chemical biology probes, as potential diagnostics and as therapeutics in the treatment of proliferative diseases including cancer and inflammation.

CROSS REFERENCE TO RELATED APPLICATION

This application claims filing benefit of U.S. Provisional PatentApplication Ser. No. 61/342,598 having a filing date of Apr. 16, 2010,which is incorporated herein in its entirety by reference.

GOVERNMENT SUPPORT CLAUSE

This invention was made with government support under RO1 CA131368-O1A2awarded by the National Institutes of Health. The government has certainrights in the invention.

BACKGROUND

CDKs, the cyclin regulatory subunits and their natural inhibitors, theCDK tumor suppressor proteins (CDKIs), are central to cell cycleregulation and their functions are commonly altered in tumor cells.Deregulation of CDK2 and CDK4 through inactivation of CDKIs such asp16^(INK4a), p21^(WAF1), p27^(KIP1), and p57^(KIP2) may override the G1checkpoint and lead to transformation. CDKs interact with certain cellcycle substrates through the cyclin binding motif (CBM) and form acomplex with the cyclin groove of the G1 and S phase cyclins, a surfacebinding site involving a protein-protein interaction. It has been shownthat CDK isoform and substrate selective inhibition may be achievedthrough the use of peptides that block recruitment of both pRb and E2Fand potently inhibit CDK2/CA kinase activity. Inhibition of CDKs thoughthe cyclin provides an approach to obtain selectivity against otherprotein kinases and inhibit only the G1 and S phase CDKs as only thesecontain a functional cyclin binding groove. In particular, CDKs thatregulate the RNA polymerase-II transcription cycle should be unaffectedby cyclin groove inhibitory (CGI) compounds. Although it has been shownthat cancer cells depend on the RNAPII cycle to express anti-apoptoticgenes and that inhibition of transcriptional CDKs leads to potentanti-tumor agents, it is at the same time likely that this will lead toeffects in normal cells and may be responsible for toxicities observedwith current CDK inhibitors being clinically evaluated.

The cyclin binding motif represents a consensus of the cyclin groovebinding sequences found in many cell cycle and tumor suppressorproteins. CGI peptides in transducible form have been shown to inducecell cycle arrest and selective apoptosis in tumor cells in vitro. Thesepermeabilized peptides also act as anti-tumor agents in that whenadministered directly to a SVT2 mouse tumor model, significant tumorgrowth inhibition was obtained and histological analysis showed thattumors underwent apoptosis.

The ATP competitive CDK inhibitors developed to date are generally nonspecific against the single variants in the CDK family. It is believedthat a major component of the anticancer activity of CDK inhibitors isthrough the transcriptional inhibition of CDK7 and 9. While it has beensuggested that transcriptional CDK inhibition may be beneficial forcancer therapy, it is also probable that this will lead to significanttoxicities. The most selective CDK inhibitor described to date is aCDK4, 6 selective compound, PD0332991 (selective vs. CDK2/proteinkinases (CDK4 IC₅₀, 0.011 μmol/L; Cdk6 IC₅₀, 0.016 μmol/L, no activityagainst 36 other protein kinases) although it has apparently not beentested against the transcriptional CDKs. Regardless, this compound is apotent antiproliferative agent against retinoblastoma (Rb)-positivetumor cells and induces a G1 arrest, with concomitant reduction ofphospho-Ser780/Ser795 on pRb. Oral administration to mice bearing theColo-205 human colon carcinoma xenografts resulted in marked tumorregression suggesting that it has significant therapeutic potential andthat targeting CDK4/cyclin D may be a viable strategy. In addition tocyclins A and E, the D-type cyclins also contain a functional cyclingroove and CDK4/cyclin D dependent kinase activities may therefore beblocked by cyclin groove inhibitors.

Further oncology target validation for selective inhibition ofCDK4/cyclin D has been demonstrated using models of breast cancer andwhere it was shown that mice lacking Cyclin D are highly resistant tomammary carcinomas induced by erbB-2 oncogene. Further research into therole of Cyclin D in tumor formation made use of a mutant form whichbinds to CDK4/6 but cannot promote catalytic activity. Thiskinase-defective Cyclin D/CDK complex results in more evidence ofresistance to erbB-2 induced tumorigenesis in mice. Combination of thesetwo studies strongly indicates that Cyclin D1/CDK4 kinase activity isrequired for erbB-2-driven tumorigenesis and therefore confirms thatCyclin D1/CDK4 is a promising oncology target. While there are severalreports of potent and selective inhibitors of the CDK2/cyclin A, Esubstrate recruitment, with both peptidic and peptidomimetic compoundsbeing identified, very little has been reported with respect to eitherinhibitors or on the requirements for binding to the cyclin groove ofCDK4,6/cyclin D1.

SUMMARY

According to one embodiment, disclosed is a method for developing apeptide inhibitor of a complex that may form between a CDK protein and acyclin D protein. For example, the method may include generating an insilico model comprising a second, different peptide inhibitor bound to asecond, different cyclin protein. For instance, the second peptideinhibitor may be a known inhibitor that may inhibit complex formationbetween the second cyclin protein and a second, different CDK protein.

The method may also include superimposing the first cyclin protein onthe in silico model and then deleting the second cyclin protein from thein silico model to form a model of the second peptide inhibitor bound tothe first cyclin protein. In addition, the deletion may be carried outin steps such that an energy minimum is converged upon.

The method may also include determining the location of conformationdifferences between the two models, i.e., the model of the cyclin Dprotein and the peptide inhibitor and the model of the second cyclinprotein and the peptide inhibitor. Based upon the conformationdifferences, the structure of the peptide inhibitor may be altered todevelop a new peptide inhibitor. Beneficially, the affinity of thecyclin D protein to this new peptide inhibitor may be greater than theaffinity of the cyclin D protein to the peptide inhibitor used in themodeling simulation.

Also disclosed are peptide inhibitors that may be formed by the method.In general, the peptide inhibitor may include one or more substitutionsand/or additions of an amino acid or a synthetic constituent as comparedto another CDK/cyclin inhibitor, e.g., the CDK/cyclin inhibitor that isused in the in silico model.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A is an alignment of binding site residues of cyclin A2 and cyclinD1.

FIG. 1B illustrates an overlay of crystal structures of cyclin D1(marked as D1; 2W96) and cyclin A2 (1OKV) illustrating similarities anddifferences of CBM contacting residues.

FIG. 1C is a ribbon representation of the overlay highlighting thedifferences in the cyclin box helices. Cyclin D1 is shown in thelightest strand and the CGI peptide is marked at either end.

FIG. 2 illustrates a correlation between IC50 and interaction energy forseveral cyclin A-peptide complexes.

FIG. 3 is a comparison of the solvent accessible surface of the cyclingrooves of A2 (FIG. 3A) and D1 (FIG. 3B).

FIG. 4 illustrates a modeled complex of the p27 residues 25-49 withcyclin D1 (2W96) overlaid with SAKRNLFGM.

DETAILED DESCRIPTION

The following description and other modifications and variations to thepresent subject matter may be practiced by those of ordinary skill inthe art, without departing from the spirit and scope of the presentdisclosure. In addition, it should be understood that aspects of thevarious embodiments may be interchanged in whole or in part.Furthermore, those of ordinary skill in the art will appreciate that theforegoing description is by way of example only, and is not intended tolimit the disclosure.

In general, disclosed herein is a strategy for inhibition of the cyclindependent kinases in anti-tumor drug discovery. More specifically,inhibition may be afforded through the substrate recruitment site on thecyclin positive regulatory subunit. This approach offers the potentialof generating cell cycle specific CDK inhibitors and reduction of theinhibition of transcription mediated through CDK7 and 9, commonlyobserved with ATP competitive compounds. While highly potent peptide andsmall molecule inhibitors of CDK2/cyclin A, E substrate recruitment havebeen reported, little information has been generated on the determinantsof inhibitor binding to the cyclin groove of the CDK4/cyclin D1 complex.CDK4/cyclin D is a validated anti-cancer drug target and it continues tobe widely pursued in the development of new therapeutics based on cellcycle blockade.

Peptides disclosed herein have been developed from investigation of thestructural basis for peptide binding to this cyclin groove andexamination of the features contributing to potency and selectivity ofinhibitors. Peptidic inhibitors of CDK4/cyclin D of pRb phosphorylationare disclosed, examples of which have been synthesized, and theircomplexes with CDK4/cyclin D1 crystal structures have been generated asfurther described herein. Comparisons of the cyclin grooves of cyclin A2and D1 are presented and provide insights in the determinants forpeptide binding and the basis for differential binding and inhibition.

In addition, a complex structure has been generated in order to modelthe interactions of the CDKI, p27^(KIP1), with cyclin D1. Thisinformation has been used to identify unique aspects of cyclin D1 thathave a significant impact on peptide interaction, and which may beexploited in the design of cyclin groove based CDK inhibitors. Peptidicand non-peptidic compounds have been synthesized in order to explorestructure-activity relationship for binding to the cyclin D1 groovewhich to date has not been carried out in a systematic fashion.Disclosed compounds may be useful as chemical biology probes todetermine the cellular and anti-tumor effects of CDK inhibitors that arecell cycle specific and do not inhibit the transcriptional regulatoryeffects of other cyclin dependent kinases. Furthermore, such compoundsmay serve as templates for structure-guided efforts to develop potentialtherapeutics based on selective inhibition of CDK4/cyclin D activity.

Common amino acid symbol abbreviations as described below in Table 1 areused throughout this disclosure.

TABLE 1 Amino Acid One letter symbol Abbreviation Alanine A Ala ArginineR Arg Asparagine N Asn Aspartic acid D Asp Cysteine C Cys Glutamine QGln Glutamic acid E Glu Glycine G Gly Histidine H His Isoleucine I IleLeucine L Leu Lysine K Lys Methionine M Met Phenylalanine F Phe ProlineP Pro Serine S Ser Threonine T Thr Tryptophan W Trp Tyrosine Y TyrValine V Val

METHODS Solid Phase Peptide Synthesis

Peptides were assembled by using standard solid phase synthesis methodon a Argonaut Quest 210 semi-automated solid phase synthesizer. 10equivalents of the C-terminal amino acid were coupled to Rink resin atthe first place using DIEA (0.082 ml) and HBTU (189.6 mg) in 5 ml DMFfor 1 h. Fmoc of the C-terminus amino acid was removed using 20%piperidine in 5 ml DMF for 10 mins before assembly of 10 equivalents ofthe next amino acid using DIEA (0.082 ml) and HBTU (189.6 mg) in 5 mlDMF. Wash cycles (5*10 ml DMF+5*10ml DCM) were applied to each step inbetween coupling and deprotection of Fmoc. Upon completion of assembly,side chain protecting groups were removed and peptides were finallycleaved from Rink resin using 90:5:5 mixtures of TFA/H₂O/TIS. Crudepeptides were purified using reverse phase flash chromatography andsemi-preparative reversed-phase HPLC methods. Pure peptides werelyophilized and characterized using mass spectrometry and analyticalHPLC. All peptides contained free amino termini and were C-terminalcarboxamides.

Computational Chemistry

Modeled complexes of peptidic cyclin groove inhibitors bound to eitherCyclin A or Cyclin D were generated as follows: SAKRRLXG series weremodeled from the crystal structure the p107 peptide bound to cyclin A(PDB: 1H28). The HAKRRLIX series were obtained by hybridizing thepeptide conformation of RRLIF (PDB: 1OKV) and SAKRRLFG (PDB: 1 H28). TheCyclin A structure in this complex was taken from 1OKV. CyclinD1/SAKRRLXG and Cyclin D/HAKRRLIX were generated in a similar mannerusing cyclin D1 crystal structures (PDB: 2W96) where the peptidicinhibitor bound to Cyclin A was superimposed with cyclin D1 and followedby deletion of Cyclin A from further minimization of the complex. Afterapplying the CHARMm forcefield in Discovery Studio 2.5 (Accelrys, SanDiego), the Smart Minimizer algorithm comprised of steepest descent andconjugate gradient and an implicit solvent model of Generalized Bornwith a simple Switching (GBSW) were applied to the complex. In general,all peptide residues were flexible. For cyclin A, all protein residueswere restrained and for cyclin D1, the backbone atoms were fixed andapproximately 300 steps of minimization were required for convergence toan energy minimum. The calculate interaction energy protocol of DS 2.5was used to generate non-bonded energy values between peptidic inhibitorand its associated cyclin. This included calculation of van der Waalsand electrostatic energies to provide an estimation of the affinity ofinhibitors

In Vitro Kinase Assay

CDK2/Cyclin A2 and CDK4/Cyclin D1 kinase assays were performed usingfull-length recombinant CDK2/cyclin A2 and CDK4/Cyclin D1 co-expressedby baculovirus in Sf9 insect cells using an N-terminal GST tag on bothproteins. The kinase assay buffer I consisted of 25 mM MOPS, pH7.2; 12.5mM beta-glycerol-phosphate, 25 mM MgCl₂, 5 mM EGTA, 2 mM EDTA and 0.25mM of DTT was added prior to use. The [³²P]-ATP Assay cocktail wasprepared in a designated radioactive working area by adding 150 μl of 10mM ATP stock solution, 100 ul[³²P]-ATP (1 mCi/100 ul), 5.75 ml of kinaseassay buffer I. 10 mM ATP Stock Solution was prepared by dissolving 55mg of ATP in 10 ml of kinase assay buffer I. Store 200 μl aliquots at−20° C. The substrate used is Rb (773-928) protein with 0.2 mg/mlconcentration. The blank control was set up by adding 10 μl of dilutedactive CDK/Cyclin with 10 μl of distilled H₂O. Otherwise, adding 10 μlof diluted active CDK/Cyclin with 10 μl of 0.2 mg/ml stock solution ofRb (773-928). The reaction was initiated by the addition of 5 μl[³²P]-ATP assay cocktail bringing the final volume up to 25 μl andincubating the mixture in a water bath at 30° C. for 15 minutes. Afterthe incubation period, the reaction was terminated by spotting 20 μl ofthe reaction mixture onto individual pre-cut strips of phophocelluloseP81 paper. The pre-cut P81 strip was air-dried and sequentially washedin a 1% phosphoric acid solution with constant gentle stirring.Radioactivity on the P81 paper was counted in the presence ofscintillation fluid on a scintillation counter. The corrected cpm wasdetermined by subtracting the blank control value for each sample andcalculating the kinase specific activity as follows: Calculation of[P³²]-ATP specific activity (SA) (cpm/pmol) Specific activity (SA)=cpmfor 5 μl [³²P]-ATP/pmoles of ATP (in 5 ul of a 250 uM ATP stocksolution). Kinase Specific Activity (SA) (pmol/min/ug ornmol/min/mg)Corrected cpm from reaction/[(SA of ³²P-ATP incpm/pmol)*(Reaction time in min)*(Enzyme amount in ug or mg)]*[(ReactionVolume)/(Spot Volume)] (SignalChem, Richmond, Canada)

RESULTS Structural Comparison of Cyclin A2 and D1 Binding Grooves

While numerous experimental structures exist for CDK2/cyclin A2 andother cyclin structures have been solved, for many years CDK4 in complexwith the D type cyclins proved refractory to crystallization. Thestructures for CDK4 in complex with cyclin D1 were recently solvedhowever only in complex with ligands binding to the ATP cleft. This dataprovided the opportunity to gain new insights into the cyclin groove ofthe D cyclins and also to determine the basis for their interactionswith cyclin groove inhibitory (CGI) peptides. At the outset of thisstudy, a limited body of data had been generated for CDK4 inhibitionwhere a series of peptides explored biologically as CDK2/cyclin A, Einhibitors were also characterized in terms of their inhibition ofcyclin D1 mediated substrate recruitment. These results determined thathighly potent peptidic CDK2 inhibitors were in general, significantlyless potent against CDK4.

In order to determine the structural and functional differences of thesecompounds, their interactions with the cyclin D1 recruitment site weremodeled and compared with known cyclin A complex structures. In terms ofcyclin A binding, optimized peptides (i.e. the octamer, HAKRRLIF, p21sequence) contain three major determinants which are required for highaffinity binding. As illustrated in FIG. 1A, these include a primaryhydrophobic pocket which interacts predominantly with leucine andphenylalanine residues of the peptide, an acidic region which formsionic contacts with basic peptide residues and a secondary hydrophobicpocket occupied by either an alanine or valine of the cyclin bindingmotif (CBM). While the majority of CGI peptide contacting residues areidentical or semi-conserved in both cyclin isotypes, two notableexceptions were observed. In cyclin D1, Val60 (interacts with Phe8) andThr62 (close to Arg4) are substituted for Leu214 and Asp216 in cyclin A2respectively. As these residues in the cyclin A context, make contactswith major determinants of cyclin A binding, it is expected that evensemi-conservative replacements would lead to significant effects oncyclin groove inhibition.

Upon overlay of the corresponding alpha carbons of the two cyclins,other semi-conserved and non-conservative differences were observed inthe structural comparison. These residues are not as significant forbinding of the octapeptide however their proximity to the cyclin bindinggroove suggests that they have potential for exploiting in the design ofselective CDK inhibitors targeting cyclin D1. Of the non peptidecontacting residues, the largest structural variation is in the exchangeof Y286 of cyclin A for 1132 of cyclin D1. Overlay and comparison of theCalpha trace of the two structures indicates that this variation,coupled with the relative movement of a helix-loop segment (residues119-136 of 2W96) leads to a significant conformation variation proximalto the cyclin groove. This region as a consequence is considerably moreopen in cyclin D1 and provides an extension to the primary hydrophobicpocket. This additional pocket could therefore accommodate larger ligandgroups than would be feasible for cyclin A inhibitors.

Sequence alignment of binding sites for cyclin A2 (top) and cyclin D1(bottom) are shown in FIG. 1A. Residues that contribute to selectivityare shown in italics. The alignment reveals that while a majority of theresidues are conserved, Leu214/Val60, Asp216/Thr62, Glu224/Glu70, andArg250/Lys96 are the main residues that are responsible for selectivity.

FIG. 1B illustrates an overlay of crystal structures of cyclin D1 (2W96)and cyclin A2 (1OKV) illustrating similarities and differences of CBMcontacting residues. The Leu and Phe residues of the CBM interactingwith the primary hydrophobic pocket are shown at 100. E220 and D216comprise the acidic region and the secondary hydrophobic pocket is tothe left of W217.

FIG. 1C is a ribbon representation of the overlay highlighting thedifferences in the cyclin box helices. Cyclin D1 is shown as the lightribbon and the ends of the CGI peptide are marked. The region displayingthe largest structural differences after superimposing the backboneatoms is marked between 101 and 102 (residues 116-136 of cyclin D1).

Another consequence of the differing conformation and composition of the116-136 region affects the secondary hydrophobic pocket with which theCGI peptide Ala2 interacts. I281 of cyclin A2 is a Tyrosine residue(Y127) in D1. The kinked helix containing this residue is shiftedtowards the groove, bringing this residue closer to the peptide anddecreasing the volume of the lipophilic pocket on the peptide N-terminalside of the W63 (FIG. 3B).

Structural Basis for Cyclin D1 Inhibition

Prior to detailed analysis of modeled peptide-cyclin D1 complexes, thestructural and energetic basis for potencies of cyclin A inhibitors wasexamined. Since a complete set of cyclin A crystal structures forpeptides with cyclin D1 affinity is not available, a cyclin A complexfor HAKRRLIF was first constructed. This peptide is highly selective forcyclin A versus cyclin D1. Formation was completed by building onexisting pentapeptide (1OKV) and octapeptide structures to supplementthose available for PVKRRLDL (E2F) and SAKRRLFG (p107) CBM sequences.The non-bonded interactions of these crystallographic complexes wereestimated by calculation of per residue and total interaction energyvalues (DS 2.5, Accelrys) to determine individual contributions and toestablish if these were reflective of the observed affinities(approximated by inhibition constants). These values shown in Table 2,below, delineated a relationship in terms of both previous SAR ofindividual residues and CGI potency.

TABLE 2 Cyclin A Cyclin A Cyclin A Cyclin A Cyclin A H −65.1 S −63.9 P−23.1 A −18.0 A −19.2 V −15.8 K −42.2 K −40.6 K −47.4 R −72.3 R −69.7 R−74.3 R −111.3 Cit −38.4 R −58.7 R −25.2 R −9.3 R −46.4 R −47.2 L −11.7L −12.8 L −9.9 L −13.8 L −13.8 I −6.8 F −12.2 D 0.6 I −0.1 I −0.06 F−23.5 G −4.2 L −15.4 F −19.5 F −19.6 total −298.3 −247.8 −194.6 −191.1−119.06 Cyclin D Cyclin D Cyclin D Cyclin D Cyclin D H −20 S −24.1 P−18.8 A −6.3 A −5.6 V −11.9 K −44.6 K −44.7 K −52.2 R −54.7 R −57 R−47.6 R −105.9 Cit −30.3 R −27 R −17.6 R −11.1 R −19.2 R −19.2 L −15.2 L−13.7 L −14.7 L −14.1 L −14.1 I 0.7 F −10.2 D −1.6 I 0.2 I 0.2 F −13 G−4.7 L −11.7 F −13.9 F 13.9 TOTAL −180.1 −177.5 −169.6 −153.9 −77.3

As determined through sensitivity to major potency loss by alaninesubstitution and other residue replacement, as shown, the energeticanalysis shows the critical Arg4 of the octapeptide makes an extensivecontribution to binding, whereas that of the less sensitive Arg5 islower. Truncation of the His-Ala-Lys N-terminal sequence has beenpreviously shown to result in a decreased affinity for cyclin A with thepotency decreasing approximately 100 fold. The contribution of thesethree residues to binding is confirmed through the energetic analysiswhere His1 and Lys3 especially provide favorable interactions with thebinding pocket. The total binding energies of both HAKRRLIF and RRLIFcalculated (−298 vs −188) correlate well with the inhibition constantsof these two compounds. Further analysis of the cyclin residueenergetics determined that acidic residues, including Asp216, Glu220,Glu224 and Asp283 allow favorable electrostatic contacts with the basicpeptide N-terminal sequence. In addition, the energetics of thecontribution of Ala2 to binding correlates well with observed potencyincrease of the Ser-Ala mutation in the p21 C-terminal context.

Further correlation of the interactions and contributions of theC-terminal sequence of the CBM interacting with the primary hydrophobicpocket (FIG. 1A) in addition to visual inspection of the non-bondedcontacts in the p21, p107 and E2F contexts, indicates the structural andenergetic differences. In varying peptide sequence contexts, the p21Leu-Ile-Phe (LIF ‘motifette’) sequence has been demonstrated to be morepotent than the p107 (and p27) LFG and E2F, LDL motifettes. Table 2illustrates that while the Leucine contributions in each context aresimilar, the Phe side chain provides increased complementarity in thep21 sequence (−23.5 kcal/mol vs. −12.2) resulting in its 2-3 foldgreater affinity compared to the LFG sequence. More favorable contactsare observed due to the geometrical arrangement of the aromatic sidechain allowed by the spacer residue between the Leu and Phe in the p21context. Overall, the energetic analysis of peptide binding to cyclin Aconfirms that a relationship exists between calculated binding enthalpyand experimental affinity and additionally that individual residueenergetics closely correlate with the SAR and contribution of CBMdeterminants. This relationship provides the basis to perform ananalysis of peptide binding to cyclin D1 and to determine the structuralbasis for decreased affinity of cyclin D1 inhibitors and therefore tofacilitate the design of more potent compounds.

The intermolecular complexes of cyclin D1 with the above peptides wereformed by superposition of the apo-cyclin D1 structure (2W96) with thecrystallographically derived cyclin A bound structure of the CBMcontaining peptides and followed by deletion of cyclin A. Theenergy-minimized structure was then calculated using the CHARMmmolecular forcefield, and the similarities and differences of cyclinbinding motif—cyclin interactions were examined.

In order to further probe the molecular consequences of variations inbinding residues, the intermolecular energies were calculated for theinteractions of each of the peptides with cyclins A and D1. In line withthe observed potencies of each compound and selectivity for cyclin A, acorrelation was determined between affinity (kinase inhibition) andtotal interaction energy (CIE) calculated for 4 peptides ranging in IC₅₀from 0.021 to 99 μM. Results are illustrated in Table 3; below and FIG.2.

TABLE 3 Interaction Energy IC50 Cyclin A (Kcal/Mol) (μM) LogIC50HAKRRLIF −298.3 0.021 −1.68 SAKRRLFG −247.8 0.073 −1.14 PVKRRLDL −194.61.2 0.08 RRLIF −191.1 7.7 0.89

For this relationship, an R² of 0.91 indicated that the both the crystaland modeled structural complexes were accurate and that the establishedcorrelation is useful as a predictive tool for design and synthesis ofmore potent and selective compounds. Comparison of the predictedaffinities of each peptide also demonstrated that the CIE correlateswell with the selectivity of the compound for cyclin A (Table 2). Thiswas additionally confirmed by a second method for estimation of bindingaffinity. Calculation of Ludi Scores provided results directly in linewith the relative potencies on A vs. D1. Further analysis of theindividual energetic contributions of residues of both the peptide andcyclin in each context revealed further evidence for the structuralbasis of CGI selectivity. Not surprisingly, it was observed that thecyclin D binding site variations described above contributed extensivelyto the selectivity of each peptide for cyclin A2. Of course, anyinhibitory peptide may be utilized in a modeling process as disclosedherein. In general, the peptide inhibitor will be relatively short, forinstance about 10 amino acids or less in length, or about 8 amino acidsor less in length, such as the octapeptides, pentapeptides, andtetrapeptides specifically detailed herein.

The optimized p21 derived peptide, HAKRRLIF is highly selective for A(0.021 μM) vs. D1 (6 μM). In addition to the total interaction energydescribing the non-bonded interactions of the peptide—cyclininteraction, the individual contributions of residues from bothmolecules was determined. These results indicate that the highly basicN-terminal residues interact much more favorably with the cyclin Agroove. As no crystal structure is available for this peptide, an Acomplex was modeled on the basis of the residue contacts of RRLIF (1OKV)and SAKRRLFG (1H28). Analysis of protein-peptide contacts andinteraction energies reveals that a greater concentration of acidicresidues in A2 compared to D1 contributes extensively to thisselectivity. In particular Asp216 of cyclin A2 (which is aligned withT62 of cyclin D1) provides a favorable addition of 17 kcal/mol to thebinding energy in interactions with Arg4. This contribution is largelyabsent in the cyclin D1 complexes modeled where the hydroxyl group ofT62 weakly interacts with Arg4. When the interaction of both Arg4 andArg5 are considered, the calculated binding energy of these two residuesfor cyclin A is more than twice that observed for cyclin D1. Glu220 inCyclin A2 interacts with Arg4 similarly to the corresponding residue(Glu66) in Cyclin D suggesting that the energetic differences are mainlydue to the absence of the second acidic residue in D.

As mentioned above, comparison of the CGI peptide binding residues incyclin D1 revealed that a valine residue occupied the position observedas a leucine in A2 (Leu214Val). As this residue is located in thelipophilic pocket interacting with the LIF motif of p21, the immediateconclusion is that this contributes significantly to peptide selectivityfor A vs D. Initially, this appears to be counterintuitive since valineis a smaller residue and might be expected to provide a larger bindingpocket. Close examination of the position of Val60 indicates that theshorter and less flexible side chain brings the interacting methylgroups closer to the phenylalanine of the peptide and thereforedecreases the volume of the hydrophobic pocket (FIGS. 1B, 3B). This wasconfirmed upon overlay of cyclin A2 bound to HAKRRLIF with the cyclin D1modeled complex, where a significant steric clash with the Phe8 sidechain was observed (FIGS. 1A, 1B). This suggests that the binding modeof Phe8 with cyclin A2 is not compatible for interaction with cyclin D.In order to determine the consequences of the overlap, the complexformed between cyclin D1 and HAKRRLIF was subjected to energyminimization to relieve this overlap. A significant displacement of thephenylalanine was observed and which did not come at the expense of Leu6(peptide residue), whose position was not affected. Further analysis ofthe interaction energy and comparison with the values calculated foroctapeptide inhibition of both cyclins, indicated a reasonablecorrelation between predicted and calculated per-residue affinity of theC-terminal motifette. These data suggest that displacement of thearomatic side chain comes at the expense of its complementarity with theprimary hydrophobic pocket and that the valine substitution isresponsible for the significant decrease in affinity for cyclin D1.

FIG. 3 is a comparison of the solvent accessible surface of the cyclingrooves of A2 (FIG. 3A) and D1 (FIG. 3B). The individual subsites of theCBG are labeled for each cyclin. Examination of the intermolecularcontacts and interaction energies for SAKRRLFG (p107 cyclin bindingmotif) with cyclin D1 reveals a similar pattern of residue energeticsfor the basic region of the peptide as in the HAKRRLIF context. SAKRRLFGhas a lower affinity for cyclin A, with the less optimal geometry of theLFG motifette resulting in a reduced contact surface area of the phenylring with the pocket. Calculation of the individual residue interactionenergies suggests that the presence of Val60 has a markedly smallerimpact on affinity of the p107 peptide for cyclin D1 than in the p21context due to the different approach angle of the interacting sidechain, and that the selectivity results from increased affinity of theArg4Arg5 determinant with cyclin A2.

Comparison of the E2F CBM, PVKRRLDL (Table 3, FIG. 3) reveals furtherinsights into the structural basis for CGI selectivity for cyclin A andafter comparison of the binding energetics again indicates lessfavorable contacts with the peptide in the cyclin D1 context (Table 2).As has been previously described, the LDL containing inhibitorsgenerally have a decreased binding relative to the LIF compounds and inthis case is reflected in the 50 fold increased IC50 value. In contrastto the LFG sequence, the LDL sequence has a substantially lowerpredicted affinity for hydrophobic pocket of cyclin D1, consistent withthe observed inhibition constants. Further analysis of peptide SAR andInsights into the design of selective cyclin D1-CDK4 inhibitors

The insights into the structural basis for peptide recognition forcyclin A and for the decreased potency against cyclin D1, providedfurther opportunity to expand inhibitor structure activity relationshipsby including additional derivatives. As suggested from the abovestructural analysis, differences in the primary hydrophobic pocket werethe major determinants in cyclin A selectivity of the studied peptides.These observations predicted that analogs with variant C-terminal groupsmay interact with the cyclin D pocket with differing affinity than tothe cyclin A groove. Based on this observation, further peptides weredesigned to exploit these structural differences and generate compoundswith increased affinity for cyclin D1. Due the decreased volume of theprimary pocket in cyclin D1, a series of non-proteinogenic cyclicreplacements for Phe7 (p107) and Phe8 (p21) cyclin binding motifcontaining octapeptides were designed. A series of 5 and 6 membered ringsystems were incorporated into the p21 (HAKRRLIX) and p107 (SAKRRLXG)contexts (Table 4, below). As shown, these included 2-furylalanine (X1),2-thienyl alanine (X2), 3-thienylalanine (X3), cyclobutylalanine (X4),cyclopentylalanine (X5), cyclohexylalanine (X6) and 3 and 4 pyridylalanine residues (X7 and X8) providing for the most part isostericfunctionalities mimicking the interactions of the phenylalanine.

The inhibition of CDK activity was determined through a standard filtercapture assay involving a GST-labeled Rb protein and quantification ofthe incorporation of 32P into the substrate. Activities of peptidespreviously tested against CDK2A and CDK4D were determined using thisassay format. Although similar constructs and substrate was used,significant differences in potency were observed. In particular the IC50for HAKRRLIF was approximately 10 fold higher than previously determined(1.3 vs. 0.14 μM) and the inhibition of CDK4/D1 was more pronounced thanbefore (1.6 vs. 6 μM). These differences may be accounted for in slightdifferences in amount of cyclin in the protein prep and excess cyclin orCDK would result in data variation. As a consequence, it was decidedthat structure-activity relationships determined using the kinase assaywere best interpreted by functional comparisons calculated relative tothe native p21 or p107 sequence in each assay. Data is thereforepresented as a ratio of each C-terminal and other analogs activity inaddition to the IC50s presented for each compound. Results are shown inTable 4, below.

TABLE 4 IC50 Po- IC50 Po- IC50 CDK2/A2 tency CDK4/D1 tency CDK2/ESEQUENCE (μM) ratio (μM) ratio (μM) p107 SAKRRLFG 3.3 2.9 SAKRRLX1G 9.12.8 7.5 2.6 4 SAKRRLX2G 27 8.2 11.4 3.9 SAKRRLX3G 1 0.3 6 2.1 SAKRRLX4G100 30.3 74 25.5 SAKRRLX5G 18 5.5 28 9.7 SAKRRLX6G 83 25.2 36 12.4SAKRRLX7G 80 24.2 51 17.6 SAKRRLX8G 750 227.3 143 49.3 p21 HAKRRLIF 1.31.5 0.3 HAKRRLIX1 6.1 4.7 11.4 7.6 1.3 HAKRRLIX2 3.6 2.8 6.5 4.3HAKRRLIX3 25 19.2 100 66.7 HAKRRLIX4 25 19.2 100 66.7 HAKRRLIX5 20 15.490 60.0 HAKRRLIX6 58 44.6 6.3 4.2 HAKRRLIX7 29 22.3 28 18.7

For the 2-furylalanine replacement (X1) in the p107 context, it wasfound that kinase activity induced by this compound decreased a similaramount in both CDK2A (2.8 fold) and CDK4D (2.6 fold) although slightlyless so for the latter. In the p21 context more of a differential wasobserved (4.7 and 7.6 fold decrease respectively). The p107 X2derivative (2-thienylalanine) data indicates that the potency decreaseagainst cyclin D was considerably reduced (3.9 fold) relative to cyclinA (8.2 fold decrease). A similar differential was observed for the p21X2 derivative (2.8 vs. 4.3 fold respectively). The X3 amino acid,3-thienylalanine was found to be less potent than X2 in both p107 andp21 contexts.

Examination of the results for aliphatic cyclic amino acid replacements,including cyclobutyl (X4), cyclopentyl (X5) and cyclohexylalanine (X6),indicated that depending on the CBM context, different selectivityprofiles were observed. X4 resulted in dramatic potency decreases inboth contexts however significantly more so with cyclin A. Both the p21and p107 versions incorporating X5, indicate that it is tolerated to alarger degree in binding to cyclin A. Conversely, the p21 derivative ofX6 is tolerated to a significantly larger degree in binding to cyclin D1with only a 4 fold drop-off observed compared to 45 fold withCDK2/cyclin A. If the IC50s of this compound are considered, it issignificantly more potent towards CDK4/cyclin D1 than againstCDK2/cyclin A (6.3 vs. 58 μM). A similar trend was shown for the p107 X6sequence although was not as dramatic. An interesting set of results wasobtained for the pyridylalanine derivatives where one carbon of thenative Phe residue is replaced with nitrogen. A large decrease inactivity was observed for these compounds in both p21 and p107 variants.Binding to cyclin D1 for these analogs was again tolerated to a largerdegree, especially with the 3-pyridylalanine derivative (X7) in the p107context. Unexpectedly, the activity of 4-pyridylalanine (X8)incorporated in SAKRRLXG decreases 200 fold relative to the nativesequence in terms of cyclin A but 46 fold in the p21 X8 derivative.Further analysis of the p21 analog binding to cyclin D1 indicates thatthe X8 containing peptide loses all activity towards CDK4/cyclin D1. Thebinding of X7 to cyclin D1 decreases 17.6 fold relative to thephenylalanine in the LXG motif and 18.7 fold in the LIX context.

Structure-Activity Relationship for Peptide Binding to Cyclin D1

For the CDK4/cyclin D1/pRb SAR of the Phe replacements in the SAKRRLXGcontext, the most potent analog is the furylalanine, X1 derivative withan IC50 of 7.5 μM with X2, the 2-thiophene containing peptide beingslightly less potent (11.4 μM). The order of potency is reversed in thep21 CBM since HAKRRLIX2 peptide has approximately 2 fold greaterinhibition than the furylalanine containing peptide (6.5 and 11.4 μMrespectively). The 3-thienyl analog X3 undergoes a potency drop offrelative to X2 in both contexts. Cyclobutylalanine incorporation intothe p107 context retained a level of binding as do HAKRRLIX5 andSAKRRLX5G although this is weak relative to the native sequences. Thecyclohexylalanine replacement, X6 was of equivalent potency to thethiophene containing peptide in the HAKRRLIX context, however of notablyhigher inhibition than the p107 derivative (6.3 μM vs 36 μM). The3-pyridylalanine peptides (X7) were considerably more significantinhibitors when incorporated C-terminal to the Ile containing spacerresidue and which has previously been shown to allow more favorablegeometry for binding. The 4-substituted derivative (X8) are weakerbinders in both CBM contexts however with 143 μM IC50 observed in theCDK4/cyclin D1 kinase assay for SAKRRLX8G and no observable activity forHAKRRLIX8. For the most part, the p21 sequences follow the previouslyobserved trend as being more potent than the p27 and p107 peptides. TwoC-terminal analogs however have higher affinity when incorporated withthe p107 residues, these being the furylalanine (X1) and4-pyridylalanine (X8) containing peptides.

Additional insights into cyclin groove interactions in cyclin D1 areprovided by C-terminal and other derivatives incorporated into HAKRRLIF.The p-fluorophenylalanine (4FPhe) derivative has been previously shownto significantly increase the inhibitory potential of peptide cyclin Ainhibitors with respect to the native residue. In contrast to theseresults, synthesis and testing of RRLI(4FPhe) resulted in decreasedinhibition of CDK4/cyclin D1 kinase activity (compared to HAKRRLIF, a160 fold decrease) vs. only a 20 fold decease in CDK2/cylin A activity).

As discussed in above sections, there are differences in the Arg4interacting residues in cyclin D1 vs. cyclin A2 and that thesevariations contribute to decreased binding of peptides to cyclin D1.Specifically, cyclin A has two acidic residues that interact with thepositively charged side chain compared to only one in cyclin D1. Thisresidue has previously been shown to be critical for cyclin A bindingactivity. It would therefore be predicted that replacement of the Argwith an isosteric residue would have less of an impact on cyclin Dbinding. Incorporation of citrullene into p21 to generate peptide,HAKCitRLIF in order to determine effect on inhibition of cyclin Dconfirmed that Arg4 is significant for interaction with cyclin D1, asshown in Table 5. The ratio the activities of the Cit and Arg containingpeptides in both contexts revealed that its effect on cyclin D1 activity(14 fold potency decrease) was similar to that observed in cyclin A.This result was corroborated by comparison of the activities ofcitrullene incorporated into pentapeptide, RCitLIF. Compared to theoctapeptide sequence, the 5 mer potency decreased roughly 120 fold forcyclin A (1.3 vs. 164 μM) and cyclin D1 (1.5 vs. 179 μM).

TABLE 5 IC50 IC50 CDK2/A2 Potency CDK4/D1 Potency SEQUENCE (μM) ratio(μM) ratio SAKRRLFG 3.3 2.9 HAKRRLIF 1.3 1.5 RRLIpfF 26 20.0 250 166.7HAKCitRLIF 18 13.8 21 14.0 HAKTRLIF 50 38.5 25 16.7 CitRLIF 164 126.2179 119.3 SCCP10 25 19.2 8 5.3 SCCP 5624 >100 60 20.7 SAKRNLFGM 146SAKRNLFG 75 SAKRALFGM 68 PAKRRLFG 8 6.7 PVKRRLFG 3 28 PVKRRL3CFG 1 3.2

Insights into SAR for interaction of cyclin D1 inhibitors of thesecondary hydrophobic was revealed through synthesis of peptidescontaining the E2F and p107 CBMs. A preference for smaller side chainswas indicated by the increased inhibition of PAKRRLFG compared to thatof PVKRRLFG. This result is in agreement with the structural analysiswhich shows a decreased volume of this subsite in cyclin D1 compared toA

From previous studies into the replacement of peptide determinants withfragment alternatives, compounds were identified where the p21 LIF motifwas replaced with a Leu-bis-aryl ether system, while maintaining asimilar potency level for cyclin A2 inhibition. A compound wassynthesized incorporating 3-phenoxybenzylamide replacing the Phe andalso N-terminally capped with1-(3,5-dichlorophenyl)-5-methyl-1H-1,2,4-triazole-3-carboxylic acid andsubsequently tested for inhibition of CDK4/D1 (SCCP10 on Table 5).SCCP10 was found to have a respectable inhibition of cyclin D1 and inaddition, its relative potency compared to the p21 octapeptide wasenhanced compared to cyclin A inhibition. SCCP10 is 5 fold less potentthan HAKRRLIF towards cyclin D1, however undergoes a 20 fold drop offwhen cyclin A2 activity is considered. A similar trend was observed forthe SAKRRL-3PBA peptide small molecule hybrid 3-phenoxybenzylamide endcapped peptide when tested against both cyclin grooves although in thiscontext the cyclin A differential was not as profound.Arg-Arg-β-homoleucyl-3-phenoxybenzylamid (SCCP 5624) was alsosynthesized and shown to be selective for CDK4/cyclin D1. The Phe sidechain of the octapeptide HAKRRLIF was replaced with smaller side chainsin a series of compounds as shown below in Table 6. SCCP396, possessingfuryl-Ala replacement was indeed selective for cyclin D1 (15% of kinaseactivity enhancement for cyclin D1 vs. A2). Other replacements withlarger ring systems (SCCP 397, 401, 402) were not as favorable. Thesmaller side chains thus reacted more favorably with cyclin D1.

Based upon the above results and other known compounds (see, e.g.,Andrews, et al. ChemBioChem, 2006, 7, 1909-1915), the N-terminalArginine of the p21 RLIF tetrapeptide was substituted with a series ofdifferent heterocyclic isosteres capable of interactions similar tocritical amino acids of the parent peptide and the triazole. Pyrazole,furan, pyrrole and thiazole systems were synthesized and varioussubstitutions of the phenyl ring were explored. The N-caps were ligatedto the tetra peptide using solid phase synthesis, purified by reversephase HPLC and characterized by MS.

In vitro binding and functional assays were performed in order to studythe inhibitory effect of compounds on CDK2/Cyclin A prior to furtherevaluation in cell viability assays to determine antitumor effects. Onthe basis of the results, further high throughput docking of potentialheterocyclic fragments was carried out to identify N-capping groups ofvarying chemical diversity for synthesis and in vitro testing.

The triazole core structure of1-(3,5-dichlorophenyl)-5-methyl-1H-1,2,4-triazole-3-carbonyl wasreplaced with isosteres such as pyrazole, furoic acid, pyrrole, andthiazole appropriately substituted with a carboxylic acid group and aphenyl ring. Fifteen capping groups were synthesized and ligated withthe tetra peptide RLIF. The synthetic schemes for pyrazoles, furan andpyrroles are outlined in scheme 1a, 1b and 1c respectively.

The X-ray crystal structure of(1-(3,5-dichlorophenyl)-5-methyl-1H-1,2,4-triazole-3-carbonyl-RLIF showsthat the N-cap hydrogen bonds with Trp217 and Gln 254 of cyclin A. SARinformation in Table 6, below reveals the following:

-   -   Triazole N-caps were found to be the most potent of the tested        compounds, followed by pyrazole and furan. The 4-chloro        substitutions on the phenyl ring are the most effective,        followed by 3,5-dichloro substituted compounds.    -   Pyrrole and thiazole show significantly lower activity than the        triazole Ncaps.

TABLE 6 CDK4/ CDK2/ cyclin cyclin D1 SCCP A IC₅₀ IC₅₀ ID R1 R2 R3 R4 W XY Z (μM) (μM) 5773 Tri- Cl H Cl CH3 N N N C  ~20  30 5774 azole H Cl HCH3 N N N C ~100  13 5762 Pyra- H H H CH₃ N N C C  ~50 5764 zole Cl H HCH₃ N N C C ~100 5771 F H H CH₃ N N C C ~100 5765 H Cl H CH₃ N N C C  395766 OCH₃ H H CH₃ N N C C ~100  120 5776 Pyr- H Cl H H N C C C >180 5775role Cl H Cl H N C C C >180 5768 Furan Cl H Cl H C O C C ~200 5772 F H HH C O C C >180 5770 H Cl H H C O C C  200 5588 OCH₃ H H H C O C C >1805587 CH₃ H H H C O C C  80 5583 Thi- H Cl H H C N C S >180 azole

Structures for each of the capping groups of Table 6 are as follows:

The validation was carried out to ensure that the method was efficientto produce reproducible results and to show that the docking results ofthe unknown compounds were predictive. Two native ligands(1-(3,5-dichlorophenyl)-5-methyl-1H-1,2,4-triazole-3-carbonyl and1-(4-chlorophenyl)-5-methyl-1H-1,2,4-triazole-3-carbonyl) and a negativecontrol were docked in both the sub units A and B of CDK2/Cyclin Acrystal structure. The variation in the parameters (i) energy grid(Dreiding, CFF and PLP1), (ii) minimization sphere (on or off) and (iii)number of poses generated (20, 10 and 5) was carried out.

For each parameter, the number of correct poses (poses that aresuperimposible with the crystal structure binding mode) of the positivecontrol ligands generated, the number of negative control poses in top25 poses, the best scoring functions that gave more number of correctposes in top ranking order were studied. The optimized parameters areenergy grid PLP1 with minimization sphere on and number of poses 10 andthe scoring function PLP1. The docking of the native ligands werereproducible with the optimized parameters. The results are shown inTable 8.

TABLE 8 Energy Grid Dreiding CFF PLP1 No. of correct 2 4 6 poses3,5-DCPT No. of correct 8 poses 4-DCPT Negative controls −PLP1(4),−PLP2(4), −PMF (7), DOCK No −ve control poses in in top 25 Jain (4),PMF(4), SCORE (6) all the scoring functions DOCK SCORE(6) Best scoringLigScore2_Dreiding PLP1, PLP2 PLP1, PLP2 function 3,5-DCPT (rank of 4, 5(for all the PLP1(9, 10, 11, 12, 25), PLP1(7, 8, 9, 10, 14, top 25scoring functions) PLP2(13, 14, 15, 16, 25) 11, 12, 13, 25),correct/closer PLP2(11, 12, 13, 14, poses for the best 18, 15, 16, 17)scoring function 4-DCPT (rank of PLP1(1, 2, 3, 4, 5, 6, 7, 8), PLP1(1,2, 3, 4, 5, 6) top 25 PLP2(17, 18, 19, 20, 21, PLP2(20, 21, 22, 23, 24,25) correct/closer 22, 23, 24) poses for the best scoring function)

Molecules may be designed on the basis of one or more of: (i) Molecularweight less than 250, (ii) absence of charge on the molecules to improvepermeation, (iii) Presence of a carboxylic acid group which is essentialfor ligation to the peptide and (iv) Commercial availability andsynthetic feasibility.

Various N-capping group designs are shown below. The scheme fordevelopment of the designs generally includes:

-   -   1. Ring A is replaced with 5 membered or six membered        heterocycles    -   2. Ring B was replaced with phenyl group or heterocycles    -   3. Spacer between two rings    -   4. Spacers before the carbonyl group.

Modeling the Interactions of p27 with Cyclin D1 Structures

CDK4/cyclin D1 have been shown to associate with p27 and that thisinteraction promotes the formation of the complex. It is also known thatdifferent states of the ternary complex exist, where p27 may bind togenerate inhibited and non-inhibited CDK4 species. A critical aspect ofthis process is the phosphorylation of p27 on Y88, sited on the 3₁₀helix which inserts into the ATP binding site of CDK4 in the inhibitedcomplex. Phosphorylation presumably leads to dissociation of the helixfrom the ATP cleft through disruption of hinge H-bonding interactionsand through repulsion of the phosphate with nearby acidic residues. Inthis non-inhibited form, p27 however, must still maintain affinity forthe complex in order to sequester the inhibitor from CDK2/cyclin Ecomplexes and allow cell cycle progression. A major contribution to thisbinding is through cyclin D1/p27 interactions and assisted by the CBMand other residues. So as to construct a model structure of p27/cyclinD1 interactions, cyclin D1 isolated from the 2W96 crystal structure wasoverlayed with the CDK2/cyclin A/p27 ternary complex (1JSU), Afterdeletion of the CDK2, cyclin A and non cyclin D1 interacting p27residues, the newly formed complex was subjected to energy minimization,After convergence of the structure to a suitable minimum, andexamination of the resulting interactions, a plausible structural basisfor the interactions of p27 with cyclin D1 interactions was described.Subsequent to generation of this structure, the interaction energies ofindividual p27 residues with cyclin D1 were generated and compared withthose for cyclin A. Significant differences in the intermolecularinteractions are apparent for several residues, several of which arenoted in the octapeptide complexes described in the above sections.These include, A28, N31, F33, V36, L41 and L45. Comparison of themolecular surface for the p27 interacting residues of cyclin A vs. thoseof cyclin D1 indicated that profound differences exist specifically inthe region where the C-terminus of the inhibitory protein exits from theprimary hydrophobic pocket. The more extensive cleft of cyclin D1, ledto the hypothesis that incorporation of a suitable residue C-terminal tothe glycine would lead to preferential binding vs. cyclin A.Computational design of a number of different residues suggested thatmethionine would be a good candidate for more optimal interactions andtherefore synthesis and testing of the p27 sequences shown in Table 5,was completed and confirmed this conclusion.

FIG. 4 illustrates a modeled complex of p27 residues 25-49 with CyclinD1 (2W96) overlayed with SAKRNLFGM. The P35 and V36 interacting site oncyclin D1 is the region shown to provide a more extensive hydrophobicpocket than in the cyclin A2 context and which was exploited bymethionine substitution. As may be seen in FIG. 4, the P35 and V36contacting site of cyclin D1 has a larger accessible volume andtherefore has suboptimal interactions with p27. This was confirmed inthe per residue interaction energy calculation which yielded values of−1.9 and −3.6 kcal/mol for D1 and A respectively. The lack of increaseof the Asparagine containing sequence may be explained by the formationof an intramolecular H-bond observed in the crystal structure and whichprecludes optimal interactions of the methionine. Substitution of thisresidue with an alanine resulted in a 2 fold potency enhancement aspredicted. As illustrated (FIG. 4), the linear side chain of the P35Manalog extends with a high degree of complementarity into the extensionof the primary hydrophobic pocket. These results suggest that thisextended binding site in cyclin D1 could be exploited in the design ofsmall molecule cyclin groove inhibitors.

In summation, comparison of the cyclin binding grooves of cyclin D1structures obtained recently through crystallographic studies providesconsiderable insight into the structural requirements for cyclin A2 vs,D1 selectivity and for differential binding of CGI peptide analogues.While the binding of peptide inhibitors of cyclin A and E substraterecruitment has been extensively characterized, little information hasbeen made available describing the determinants of cyclin D inhibition.Structural analysis revealed that two key amino acid substitutions inthe cyclin D1 groove have a major impact on peptide inhibitor binding.Exchange of one of the two acidic residues interacting with Arg4 (Asp216and Glu220), with Thr62 significantly decreases the calculated enthalpiccontribution to binding and is suggestive of a large decrease inaffinity. In order to determine if the predicted decrease in theelectrostatic interaction energy is significant in contributing tocyclin A selectivity, the arginine isostere citrullene was incorporatedinto the p21 8mer, HAKCitRLIF (Table 5). It was predicted that due tothe less acidic environment of the Arg contacting residues in cyclin D,that the potency decrease would be less marked in this context. Inreality however, a similar drop off was demonstrated in both scenariosand thus indicating otherwise. Closer examination of the peptide-cyclinD1 structure suggests that the urea carbonyl of citrullene is withinH-bonding distance of the OH group of Thr62. This interaction wouldtherefore compensate for the decreased capacity to ion pair and resultin a similar potency decrease.

As described, the second major difference between the two cyclins is inthe exchange of Leu214 in cyclin A for Val60 in cyclin D. The smallerValine sidechain projects down toward the base of this hydrophobicpocket with the net effect that the □ methyis are brought into closerproximity to the peptide inhibitor side chains which insert into thispocket. This substitution therefore decreases the volume of the primaryhydrophobic pocket in the latter and thereby results in lower affinityof CGI peptides containing phenylalanine. Cyclin bound complexes weregenerated for a series of peptides previously determined to have varyingaffinities for cyclin A and cyclin D1 and possessing differentC-terminal sequences. The calculated binding energies for thesecomplexes correlated well not only for IC50s determined for cyclin A andD1 individually but also for the selectivity of the peptides observed.These results therefore determined that in addition to the X-raystructures used, the model structures for the peptide-cyclin complexesgave valid results and that this information is useful in the potentialdesign and optimization of improved cyclin D1 inhibitors. From theseobservations, the hypothesis was proposed that due to the decreasedvolume of the primary hydrophobic pocket relative to cyclin A, that theincorporation of non-natural amino acids with differing cyclicsidechains than phenylalanine might be tolerated to a greater degree. Tothis end, the results presented confirm that this is indeed the casehowever these are dependent on the peptide context. As has beenpreviously structurally characterized, the presence of a spacer residuebetween the critical Leu and Phe functions to allow a geometricalarrangement of the two side chains that interacts with a greater degreeof complementarity and therefore increases binding affinity relative topeptides with no spacer. The results suggest that non-spacer containingpeptide, SAKRRLXG, has a binding mode which is more conducive andtolerant of smaller cyclic sidechains. In order to probe this further, a3D structure for each of the synthesized analogs in complex with bothcyclins was generated and further to this, their non-bonded interactionenergy calculated. These results suggested that a correlation betweenthe observed potencies and the calculated affinity existed and confirmedthat for both 5 membered rings, a decrease in binding of these analogueswould be expected. The structural basis for the greater affinity of thefurylalanine (X1) vs. the 2-thienylalanine (X2) in the p107 context isapparent from the modeled structure. The closer proximity of theheteroatom to Val60 in the peptide without the spacer residue results indisplacement of the larger sulfur containing Phe replacement (thiophenering) and lower relative affinity. In the p21 peptide, theconformational preference allowed by the spacer residue, results in theheteroatom pointing to the back wall of the primary hydrophobic pocket,away from Val60. As the heteroatom projects into more expansive region,the larger sulfur atom provides greater complementarity with K96 andQ100 resulting in increased affinity in the thienylalanine derivative.Changing the context of the heterocyclic sulfur atom as in X3 resultedin potency increase of SAKRRLX3G for cyclin A but an increase in cyclinD1 affinity. The larger hydrophobic pocket in cyclin A may accommodatethe bulky sulfur atom more readily than may the cyclin D1 site decreasedin volume by Val60. Examination of the intermolecular contacts for thecyclohexylalanine derivative X6, a bulkier Phe replacement as a resultof the unsaturated ring, again provided insight into the differingpotencies for peptides containing this residue with cyclin D1. Modelingof the complex of SAKRRLX6G with cyclin D1 (12 fold decrease in IC50),suggested that in order to maintain productive binding, the CHAsidechain is brought in close proximity to Val60 resulting inunfavorable contacts. For the HAKRRLIX6 inhibitor (4 fold loss inpotency), the sidechain may adopt a more favorable position, contactingseveral residues of the primary binding site in line with its higherrelative potency. The dramatic decreases in inhibition of thepyridylalanine derivatives X7 and X8 relative to the nativephenylalanine cannot readily explained in terms of differentinteractions with the cyclin groove. A probable scenario is that thepyridyl ring is solvated to a greater degree relative to the phenyl andtherefore a desolvation penalty would disfavor binding. A number ofsubstitutions in the cyclin groove recognition motif have beenincorporated in the N-terminal and arginine binding site and provideadditional information on the tolerance of sequence changes upon bindingto the secondary hydrophobic and acidic regions of cyclin D1.

While the subject matter has been described in detail with respect tothe specific embodiments thereof, it will be appreciated that thoseskilled in the art, upon attaining an understanding of the foregoing,may readily conceive of alterations to, variations of, and equivalentsto these embodiments. Accordingly, the scope of the present disclosureshould be assessed as that of the appended claims and any equivalentsthereto.

1. A method for developing a first peptide inhibitor of a complex formedbetween a first CDK protein and a first cyclin protein, the first cyclinprotein being a cyclin D protein, the method comprising: generating anin silico model comprising a second peptide inhibitor bound to a secondcyclin protein, the second peptide inhibitor inhibiting complexformation between the second cyclin protein and a second CDK protein;superimposing the first cyclin protein on the in silico model; deletingthe second cyclin protein from the in silico model to form a model ofthe second peptide inhibitor bound to the first cyclin protein, whereinthe deletion is carried out in steps such that an energy minimum isconverged upon; determining the location of conformation differencesbetween the model of the first cyclin protein and the second peptideinhibitor and the model of the second cyclin protein and the secondpeptide inhibitor; and altering the structure of the second peptideinhibitor to develop the first peptide inhibitor, wherein the affinityof the first cyclin protein to the first peptide inhibitor is greaterthan the affinity of the first cyclin protein to the second peptideinhibitor.
 2. The method according to claim 1, wherein the first cyclinprotein is a cyclin D1 protein.
 3. The method according to claim 1,wherein the second cyclin protein is a cyclin A protein.
 4. The methodaccording to claim 3, wherein the second cyclin protein is a cyclin A2protein.
 5. The method according to claim 1, wherein the first CDKprotein is a CDK4 protein.
 6. The method according to claim 1, whereinthe second CDK protein is a CDK2 protein.
 7. The method according toclaim 1, wherein all peptide residues of the models are flexible.
 8. Themethod according to claim 1, wherein the second peptide inhibitorcomprises less than about 10 amino acids.
 9. The method according toclaim 1, wherein the step of altering the structure of the secondpeptide inhibitor comprises substituting an amino acid of the secondpeptide inhibitor with a different amino acid or a syntheticsubstituent.
 10. The method according to claim 1, wherein the step ofaltering the structure of the second peptide inhibitor comprises addingan amino acid or a synthetic substituent to an end of the second peptideinhibitor.
 11. The method according to claim 1, wherein the secondpeptide inhibitor is selected from the group consisting of HAKRRLIF,SAKRRLFG, PVKRRLDL, and RRLIF.
 12. The method according to claim 1,wherein the step of altering the structure of the second peptideinhibitor comprises altering the N-terminus of the second peptideinhibitor.
 13. A peptide inhibitor that inhibits complex formationbetween a CDK4 protein and a cyclin D protein, the peptide inhibitorbeing a derivative of a second CDK/cyclin inhibitor, the peptideinhibitor comprising one or more substitutions and/or additions of anamino acid or a synthetic constituent as compared to the secondCDK/cyclin inhibitor.
 14. The peptide inhibitor according to claim 13,wherein the second CDK/cyclin inhibitor is a CDK2/cyclin inhibitor. 15.The peptide inhibitor according to claim 14, wherein the secondCDK/cyclin inhibitor is a CDK2/cyclin A inhibitor.
 16. The peptideinhibitor according to claim 13, wherein the second CDK/cyclin inhibitoris an octapeptide CDK/cyclin inhibitor that includes a phenylalanineresidue in at least one of the seventh and eighth position of theoctapeptide, the peptide inhibitor comprising a non-proteinoginic cyclicsubstituent in place of the phenylalanine residue of the octapeptideCDK/cyclin A2 inhibitor.
 17. The peptide inhibitor according to claim16, the non-proteinoginic cyclic substituent being selected from one ofthe following:


18. The peptide inhibitor according to claim 16, wherein the octapeptideCDK/cyclinA2 inhibitor is SAKRRLFG or HAKRRLIF.
 19. The peptideinhibitor according to claim 16, wherein the non-proteinoginic cyclicsubstituent is


20. The peptide inhibitor according to claim 13, wherein the peptideinhibitor includes a substitution of an amino acid with3-phenoxybenzylamide as compared to the second CDK/cyclin inhibitor. 21.The peptide inhibitor according to claim 13, wherein the peptideinhibitor includes a terminal N-cap that is not present on the secondCDK/cyclin inhibitor.
 22. The peptide inhibitor according to claim 21,wherein the terminal N-cap is1-(3,5-dichlorophenyl)-5-methyl-1H-1,2,4-triazole-3-carboxylic acid or aderivative thereof in which the triazole core is replaced with anisostere.
 23. The peptide inhibitor according to claim 22, in which theisostere is a pyrazole, furoic acid, pyrrole, or thiazole.
 24. Thepeptide inhibitor according to claim 13, in which the peptide inhibitorincludes a substitution of an amino acid as compared to the secondCDK/cyclin inhibitor, the amino acid substitution including a smallerside chain as compared to the amino acid of the CDK/cyclin inhibitor.25. The peptide inhibitor according to claim 13, wherein thesubstitution or addition is a synthetic constituent having the structureof:


26. The peptide inhibitor according to claim 13, wherein thesubstitution or addition is a synthetic constituent having the structureof: